AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0591260


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 63 sgRNAs with CRISPR-Local

Find 81 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAAGAAACAATGACGGTATC+TGG 0.223499 4_2:-15586221 Msa0591250:intron
CGCTTTACGCCCAATCATTC+CGG 0.287091 4_2:+15586136 Msa0591260:CDS
TCCTTTCGCTCCTCAGCTTA+CGG 0.318574 4_2:+15586478 Msa0591260:CDS
ATCAGACGCGAGCCCCTCCT+TGG 0.323688 4_2:+15586446 Msa0591260:CDS
CTCTGTCTTACCGCGGCTGC+TGG 0.335301 4_2:+15586173 Msa0591260:CDS
CCTTTCGCTCCTCAGCTTAC+GGG 0.341229 4_2:+15586479 Msa0591260:CDS
CAAGCGTTATCCGGAATGAT+TGG 0.365557 4_2:-15586146 Msa0591250:CDS
ACCGTCATTGTTTCTTCTCC+AGG 0.384151 4_2:+15586227 Msa0591260:CDS
CAGCTGTTGTTCCCCTCCCA+AGG 0.401225 4_2:+15586519 Msa0591260:CDS
CAGAGGATGCAAGCGTTATC+CGG 0.442617 4_2:-15586155 Msa0591250:CDS
GGTTGAGCCCTGGGATTTGA+CGG 0.443812 4_2:+15586089 None:intergenic
CTTGGGAGGGGAACAACAGC+TGG 0.448224 4_2:-15586518 Msa0591250:intron
CTCGCGTCTGATTAGCTAGT+TGG 0.450357 4_2:-15586435 Msa0591250:intron
GTTGTTCCCCTCCCAAGGGC+AGG 0.453286 4_2:+15586524 Msa0591260:CDS
TCAGACGCGAGCCCCTCCTT+GGG 0.455699 4_2:+15586447 Msa0591260:CDS
TAAGTTCGCCGTCAAATCCC+AGG 0.467544 4_2:-15586097 Msa0591250:CDS
TAAGAACCTGCCCTTGGGAG+GGG 0.474163 4_2:-15586530 Msa0591250:intron
AGGGGAACAACAGCTGGAAA+CGG 0.479232 4_2:-15586512 Msa0591250:intron
TTTACACATGCAAGTCGAAC+GGG 0.480570 4_2:-15586590 Msa0591250:CDS
AAGAAACAATGACGGTATCT+GGG 0.492143 4_2:-15586220 Msa0591250:intron
AACGCGTAAGAACCTGCCCT+TGG 0.497667 4_2:-15586536 Msa0591250:intron
AGGAGGAATCCGCCCAAGGA+GGG 0.502243 4_2:-15586459 Msa0591250:intron
TGGTGTTTCCAGTGGCGGAC+GGG 0.506464 4_2:-15586564 Msa0591250:intron
AAGCGTTATCCGGAATGATT+GGG 0.511219 4_2:-15586145 Msa0591250:CDS
CATGCAAGTCGAACGGGAAG+TGG 0.511388 4_2:-15586584 Msa0591250:CDS
GTTACTCACCCGTCCGCCAC+TGG 0.515654 4_2:+15586556 Msa0591260:CDS
GTGGTGTTTCCAGTGGCGGA+CGG 0.521309 4_2:-15586565 Msa0591250:CDS
ACGCGTAAGAACCTGCCCTT+GGG 0.530469 4_2:-15586535 Msa0591250:intron
AGCTGTTGTTCCCCTCCCAA+GGG 0.533909 4_2:+15586520 Msa0591260:CDS
CCAAGGCGGTGATCAGTAGC+TGG 0.540351 4_2:-15586397 Msa0591250:intron
TAACTCTGTGCCAGCAGCCG+CGG 0.544469 4_2:-15586183 Msa0591250:intron
CGTAAGAACCTGCCCTTGGG+AGG 0.550231 4_2:-15586532 Msa0591250:intron
CCCGTAAGCTGAGGAGCGAA+AGG 0.554829 4_2:-15586479 Msa0591250:intron
GAGAGGATGATCAGCCACAC+TGG 0.556699 4_2:-15586371 Msa0591250:intron
GTAAGAACCTGCCCTTGGGA+GGG 0.557080 4_2:-15586531 Msa0591250:intron
GGAGGAATCCGCCCAAGGAG+GGG 0.562553 4_2:-15586458 Msa0591250:intron
AAGTTCGCCGTCAAATCCCA+GGG 0.564420 4_2:-15586096 Msa0591250:CDS
GACGCGAGCCCCTCCTTGGG+CGG 0.572606 4_2:+15586450 Msa0591260:CDS
CTTTCGCTCCTCAGCTTACG+GGG 0.577687 4_2:+15586480 Msa0591260:CDS
CCAGCTACTGATCACCGCCT+TGG 0.578071 4_2:+15586397 Msa0591260:CDS
GGGCGTAAAGCGTCTGTAGG+TGG 0.587281 4_2:-15586125 Msa0591250:CDS
AGTGTGGCTGATCATCCTCT+CGG 0.593369 4_2:+15586373 Msa0591260:CDS
CGAAAGGAGGAATCCGCCCA+AGG 0.596152 4_2:-15586463 Msa0591250:intron
CTTTACACATGCAAGTCGAA+CGG 0.597034 4_2:-15586591 Msa0591250:CDS
TCCTGGCTCAGGATGAACGC+TGG 0.603603 4_2:-15586621 Msa0591250:CDS
AGAGGATGATCAGCCACACT+GGG 0.612353 4_2:-15586370 Msa0591250:intron
TGCTAATACCCCGTAAGCTG+AGG 0.615470 4_2:-15586488 Msa0591250:intron
GGTATCTGGGGAATAAGCAT+CGG 0.620214 4_2:-15586207 Msa0591250:intron
ACGGGAAGTGGTGTTTCCAG+TGG 0.620953 4_2:-15586572 Msa0591250:CDS
AAGGAGGAATCCGCCCAAGG+AGG 0.622334 4_2:-15586460 Msa0591250:intron
GGAAGTGGTGTTTCCAGTGG+CGG 0.627120 4_2:-15586569 Msa0591250:CDS
TCCTGGAGAAGAAACAATGA+CGG 0.628601 4_2:-15586228 Msa0591250:intron
ATTGGGCGTAAAGCGTCTGT+AGG 0.632255 4_2:-15586128 Msa0591250:CDS
GTCTGATTAGCTAGTTGGTG+AGG 0.641304 4_2:-15586430 Msa0591250:intron
CAGCAGCCGCGGTAAGACAG+AGG 0.650015 4_2:-15586172 Msa0591250:CDS
TGGCTCAGGATGAACGCTGG+CGG 0.650788 4_2:-15586618 Msa0591250:CDS
GTAAGCTGAGGAGCGAAAGG+AGG 0.654589 4_2:-15586476 Msa0591250:intron
GCCTTGTCTCAGTCCCAGTG+TGG 0.654955 4_2:+15586357 Msa0591260:intron
AGAAACAATGACGGTATCTG+GGG 0.658343 4_2:-15586219 Msa0591250:intron
TGATCAGTAGCTGGTCCGAG+AGG 0.705254 4_2:-15586388 Msa0591250:intron
GGTGAGGTAATAGCTTACCA+AGG 0.724474 4_2:-15586414 Msa0591250:intron
GAGGTAATAGCTTACCAAGG+CGG 0.748896 4_2:-15586411 Msa0591250:intron
TTGCATCCTCTGTCTTACCG+CGG 0.760348 4_2:+15586166 Msa0591260:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AAGAAACAATGACGGTATCT+GGG - chr4_2:15586223-15586242 Msa0591250:intron 35.0%
AAAAGAATTTCATGACCCGT+AGG + chr4_2:15586250-15586269 Msa0591260:intron 35.0%
AAGCGTTATCCGGAATGATT+GGG - chr4_2:15586148-15586167 Msa0591250:CDS 40.0%
AGAAACAATGACGGTATCTG+GGG - chr4_2:15586222-15586241 Msa0591250:intron 40.0%
GAAGAAACAATGACGGTATC+TGG - chr4_2:15586224-15586243 Msa0591250:intron 40.0%
TCCTGGAGAAGAAACAATGA+CGG - chr4_2:15586231-15586250 Msa0591250:intron 40.0%
! GGGTCATGAAATTCTTTTCC+TGG - chr4_2:15586248-15586267 Msa0591250:intron 40.0%
TTTACACATGCAAGTCGAAC+GGG - chr4_2:15586593-15586612 Msa0591250:CDS 40.0%
CTTTACACATGCAAGTCGAA+CGG - chr4_2:15586594-15586613 Msa0591250:CDS 40.0%
CAAGCGTTATCCGGAATGAT+TGG - chr4_2:15586149-15586168 Msa0591250:CDS 45.0%
GGTATCTGGGGAATAAGCAT+CGG - chr4_2:15586210-15586229 Msa0591250:intron 45.0%
! ACCGTCATTGTTTCTTCTCC+AGG + chr4_2:15586227-15586246 Msa0591260:CDS 45.0%
! AGTGGGGAATTTTCCGCAAT+GGG - chr4_2:15586315-15586334 Msa0591250:CDS 45.0%
GAGGTAATAGCTTACCAAGG+CGG - chr4_2:15586414-15586433 Msa0591250:intron 45.0%
GGTGAGGTAATAGCTTACCA+AGG - chr4_2:15586417-15586436 Msa0591250:intron 45.0%
! GTCTGATTAGCTAGTTGGTG+AGG - chr4_2:15586433-15586452 Msa0591250:intron 45.0%
! ATTGGGCGTAAAGCGTCTGT+AGG - chr4_2:15586131-15586150 Msa0591250:CDS 50.0%
CGCTTTACGCCCAATCATTC+CGG + chr4_2:15586136-15586155 Msa0591260:CDS 50.0%
CAGAGGATGCAAGCGTTATC+CGG - chr4_2:15586158-15586177 Msa0591250:CDS 50.0%
TTGCATCCTCTGTCTTACCG+CGG + chr4_2:15586166-15586185 Msa0591260:CDS 50.0%
! CAGTGGGGAATTTTCCGCAA+TGG - chr4_2:15586316-15586335 Msa0591250:CDS 50.0%
AGAGGATGATCAGCCACACT+GGG - chr4_2:15586373-15586392 Msa0591250:intron 50.0%
AGTGTGGCTGATCATCCTCT+CGG + chr4_2:15586373-15586392 Msa0591260:CDS 50.0%
! CTCGCGTCTGATTAGCTAGT+TGG - chr4_2:15586438-15586457 Msa0591250:intron 50.0%
TCCTTTCGCTCCTCAGCTTA+CGG + chr4_2:15586478-15586497 Msa0591260:CDS 50.0%
TGCTAATACCCCGTAAGCTG+AGG - chr4_2:15586491-15586510 Msa0591250:intron 50.0%
AGGGGAACAACAGCTGGAAA+CGG - chr4_2:15586515-15586534 Msa0591250:intron 50.0%
CGTGGAGGTAAAAGGCCTAC+GGG - chr4_2:15586268-15586287 Msa0591250:intron 55.0%
GCGTGGAGGTAAAAGGCCTA+CGG - chr4_2:15586269-15586288 Msa0591250:intron 55.0%
! GTAGGCCTTTTACCTCCACG+CGG + chr4_2:15586268-15586287 Msa0591260:intron 55.0%
CAATGCCGCGTGGAGGTAAA+AGG - chr4_2:15586276-15586295 Msa0591250:intron 55.0%
AGACAAGGCCCAGACTCCTA+CGG - chr4_2:15586346-15586365 Msa0591250:intron 55.0%
GAGAGGATGATCAGCCACAC+TGG - chr4_2:15586374-15586393 Msa0591250:intron 55.0%
TGATCAGTAGCTGGTCCGAG+AGG - chr4_2:15586391-15586410 Msa0591250:intron 55.0%
GTAAGCTGAGGAGCGAAAGG+AGG - chr4_2:15586479-15586498 Msa0591250:intron 55.0%
CCTTTCGCTCCTCAGCTTAC+GGG + chr4_2:15586479-15586498 Msa0591260:CDS 55.0%
CTTTCGCTCCTCAGCTTACG+GGG + chr4_2:15586480-15586499 Msa0591260:CDS 55.0%
AGCTGTTGTTCCCCTCCCAA+GGG + chr4_2:15586520-15586539 Msa0591260:CDS 55.0%
TAAGAACCTGCCCTTGGGAG+GGG - chr4_2:15586533-15586552 Msa0591250:intron 55.0%
GTAAGAACCTGCCCTTGGGA+GGG - chr4_2:15586534-15586553 Msa0591250:intron 55.0%
ACGCGTAAGAACCTGCCCTT+GGG - chr4_2:15586538-15586557 Msa0591250:intron 55.0%
AACGCGTAAGAACCTGCCCT+TGG - chr4_2:15586539-15586558 Msa0591250:intron 55.0%
GGAAGTGGTGTTTCCAGTGG+CGG - chr4_2:15586572-15586591 Msa0591250:CDS 55.0%
ACGGGAAGTGGTGTTTCCAG+TGG - chr4_2:15586575-15586594 Msa0591250:CDS 55.0%
CATGCAAGTCGAACGGGAAG+TGG - chr4_2:15586587-15586606 Msa0591250:CDS 55.0%
! GGGCGTAAAGCGTCTGTAGG+TGG - chr4_2:15586128-15586147 Msa0591250:CDS 60.0%
TAACTCTGTGCCAGCAGCCG+CGG - chr4_2:15586186-15586205 Msa0591250:intron 60.0%
CGCAATGGGCGAAAGCCTGA+CGG - chr4_2:15586301-15586320 Msa0591250:CDS 60.0%
CGTCAGGCTTTCGCCCATTG+CGG + chr4_2:15586299-15586318 Msa0591260:intron 60.0%
GACAAGGCCCAGACTCCTAC+GGG - chr4_2:15586345-15586364 Msa0591250:intron 60.0%
GCCTTGTCTCAGTCCCAGTG+TGG + chr4_2:15586357-15586376 Msa0591260:intron 60.0%
GCCACACTGGGACTGAGACA+AGG - chr4_2:15586361-15586380 Msa0591250:intron 60.0%
CCAAGGCGGTGATCAGTAGC+TGG - chr4_2:15586400-15586419 Msa0591250:intron 60.0%
CCAGCTACTGATCACCGCCT+TGG + chr4_2:15586397-15586416 Msa0591260:CDS 60.0%
AGGAGGAATCCGCCCAAGGA+GGG - chr4_2:15586462-15586481 Msa0591250:intron 60.0%
AAGGAGGAATCCGCCCAAGG+AGG - chr4_2:15586463-15586482 Msa0591250:intron 60.0%
CGAAAGGAGGAATCCGCCCA+AGG - chr4_2:15586466-15586485 Msa0591250:intron 60.0%
CCCGTAAGCTGAGGAGCGAA+AGG - chr4_2:15586482-15586501 Msa0591250:intron 60.0%
CTTGGGAGGGGAACAACAGC+TGG - chr4_2:15586521-15586540 Msa0591250:intron 60.0%
CAGCTGTTGTTCCCCTCCCA+AGG + chr4_2:15586519-15586538 Msa0591260:CDS 60.0%
CGTAAGAACCTGCCCTTGGG+AGG - chr4_2:15586535-15586554 Msa0591250:intron 60.0%
!! TGGTGTTTCCAGTGGCGGAC+GGG - chr4_2:15586567-15586586 Msa0591250:CDS 60.0%
! GTGGTGTTTCCAGTGGCGGA+CGG - chr4_2:15586568-15586587 Msa0591250:CDS 60.0%
CAGCAGCCGCGGTAAGACAG+AGG - chr4_2:15586175-15586194 Msa0591250:intron 65.0%
CTCTGTCTTACCGCGGCTGC+TGG + chr4_2:15586173-15586192 Msa0591260:CDS 65.0%
TCCTACGGGAGGCAGCAGTG+GGG - chr4_2:15586331-15586350 Msa0591250:CDS 65.0%
CTCCTACGGGAGGCAGCAGT+GGG - chr4_2:15586332-15586351 Msa0591250:CDS 65.0%
ACTCCTACGGGAGGCAGCAG+TGG - chr4_2:15586333-15586352 Msa0591250:CDS 65.0%
TGCTGCCTCCCGTAGGAGTC+TGG + chr4_2:15586334-15586353 Msa0591260:intron 65.0%
GCTGCCTCCCGTAGGAGTCT+GGG + chr4_2:15586335-15586354 Msa0591260:intron 65.0%
AAGGCCCAGACTCCTACGGG+AGG - chr4_2:15586342-15586361 Msa0591250:CDS 65.0%
ATCAGACGCGAGCCCCTCCT+TGG + chr4_2:15586446-15586465 Msa0591260:CDS 65.0%
TCAGACGCGAGCCCCTCCTT+GGG + chr4_2:15586447-15586466 Msa0591260:CDS 65.0%
GGAGGAATCCGCCCAAGGAG+GGG - chr4_2:15586461-15586480 Msa0591250:intron 65.0%
GTTGTTCCCCTCCCAAGGGC+AGG + chr4_2:15586524-15586543 Msa0591260:CDS 65.0%
GTTACTCACCCGTCCGCCAC+TGG + chr4_2:15586556-15586575 Msa0591260:CDS 65.0%
GACGGAGCAATGCCGCGTGG+AGG - chr4_2:15586283-15586302 Msa0591250:CDS 70.0%
CCTGACGGAGCAATGCCGCG+TGG - chr4_2:15586286-15586305 Msa0591250:CDS 70.0%
CCACGCGGCATTGCTCCGTC+AGG + chr4_2:15586283-15586302 Msa0591260:intron 70.0%
TCCCCACTGCTGCCTCCCGT+AGG + chr4_2:15586327-15586346 Msa0591260:intron 70.0%
GACGCGAGCCCCTCCTTGGG+CGG + chr4_2:15586450-15586469 Msa0591260:CDS 75.0%
Chromosome Type Strat End Strand Name
chr4_2 gene 15586098 15586636 15586098 ID=Msa0591260;Name=Msa0591260
chr4_2 mRNA 15586098 15586636 15586098 ID=Msa0591260-mRNA-1;Parent=Msa0591260;Name=Msa0591260-mRNA-1;_AED=0.46;_eAED=0.52;_QI=0|0|0|1|1|1|2|0|145
chr4_2 exon 15586098 15586267 15586098 ID=Msa0591260-mRNA-1:exon:4491;Parent=Msa0591260-mRNA-1
chr4_2 exon 15586369 15586636 15586369 ID=Msa0591260-mRNA-1:exon:4492;Parent=Msa0591260-mRNA-1
chr4_2 CDS 15586098 15586267 15586098 ID=Msa0591260-mRNA-1:cds;Parent=Msa0591260-mRNA-1
chr4_2 CDS 15586369 15586636 15586369 ID=Msa0591260-mRNA-1:cds;Parent=Msa0591260-mRNA-1
Gene Sequence

>Msa0591260

CTGGGATTTGACGGCGAACTTAAAAAGCCACCTACAGACGCTTTACGCCCAATCATTCCGGATAACGCTTGCATCCTCTGTCTTACCGCGGCTGCTGGCACAGAGTTAGCCGATGCTTATTCCCCAGATACCGTCATTGTTTCTTCTCCAGGAAAAGAATTTCATGACCCTCCCAGTGTGGCTGATCATCCTCTCGGACCAGCTACTGATCACCGCCTTGGTAAGCTATTACCTCACCAACTAGCTAATCAGACGCGAGCCCCTCCTTGGGCGGATTCCTCCTTTCGCTCCTCAGCTTACGGGGTATTAGCAGCCGTTTCCAGCTGTTGTTCCCCTCCCAAGGGCAGGTTCTTACGCGTTACTCACCCGTCCGCCACTGGAAACACCACTTCCCGTTCGACTTGCATGTGTAAAGCATGCCGCCAGCGTTCATCCTGA

Protein sequence

>Msa0591260

LGFDGELKKPPTDALRPIIPDNACILCLTAAAGTELADAYSPDTVIVSSPGKEFHDPPSVADHPLGPATDHRLGKLLPHQLANQTRAPPWADSSFRSSAYGVLAAVSSCCSPPKGRFLRVTHPSATGNTTSRSTCMCKACRQRSS*